library(tidyverse)
library(targets)
library(kableExtra)
Leaf disc vs whole-leaf LMA (species-level)
Pooled
Seprated
coef
SMA table
species
tar_load(sma_sp_tab)
sma_sp_tab |>
kable() |>
kable_styling()
|
Data
|
Slope
|
Intercept
|
R2
|
|
All
|
0.97 [0.94, 1.01]
|
0.09 [0.02, 0.16]
|
0.87
|
|
Thick~Large
|
0.93 [0.85, 1.03]
|
0.19 [0.01, 0.37]
|
0.86
|
|
Thick~Small
|
1.02 [0.97, 1.07]
|
0 [-0.11, 0.11]
|
0.93
|
|
Thin~Large
|
0.91 [0.82, 1.02]
|
0.2 [0.02, 0.37]
|
0.71
|
|
Thin~Small
|
0.93 [0.83, 1.03]
|
0.16 [-0.02, 0.35]
|
0.84
|
species LD
tar_load(sma_sp_ld_tab)
sma_sp_ld_tab |>
kable() |>
kable_styling()
|
Data
|
Slope
|
Intercept
|
R2
|
|
All
|
0.97 [0.94, 1.01]
|
0.09 [0.02, 0.16]
|
0.87
|
|
Dense ~ Thick~Large
|
0.96 [0.82, 1.13]
|
0.14 [-0.15, 0.43]
|
0.79
|
|
Dense ~ Thick~Small
|
1.02 [0.94, 1.11]
|
-0.01 [-0.17, 0.15]
|
0.90
|
|
Dense ~ Thin~Large
|
0.8 [0.66, 0.98]
|
0.37 [0.09, 0.64]
|
0.60
|
|
Dense ~ Thin~Small
|
0.86 [0.72, 1.03]
|
0.27 [-0.01, 0.55]
|
0.81
|
|
Nondense ~ Thick~Large
|
0.75 [0.59, 0.94]
|
0.58 [0.22, 0.94]
|
0.72
|
|
Nondense ~ Thick~Small
|
0.99 [0.87, 1.13]
|
0.05 [-0.23, 0.32]
|
0.82
|
|
Nondense ~ Thin~Large
|
0.77 [0.65, 0.91]
|
0.49 [0.25, 0.74]
|
0.56
|
|
Nondense ~ Thin~Small
|
0.87 [0.71, 1.06]
|
0.28 [-0.06, 0.62]
|
0.68
|
tree
tar_load(sma_tree_tab)
sma_tree_tab |>
kable() |>
kable_styling()
|
Data
|
Slope
|
Intercept
|
R2
|
|
All
|
0.96 [0.94, 0.99]
|
0.11 [0.06, 0.16]
|
0.72
|
|
Thick~Large
|
0.97 [0.9, 1.04]
|
0.12 [-0.03, 0.26]
|
0.61
|
|
Thick~Small
|
0.94 [0.9, 0.98]
|
0.16 [0.07, 0.24]
|
0.79
|
|
Thin~Large
|
0.91 [0.84, 0.97]
|
0.21 [0.09, 0.32]
|
0.45
|
|
Thin~Small
|
0.91 [0.85, 0.98]
|
0.19 [0.07, 0.31]
|
0.66
|
tree LD
tar_load(sma_tree_ld_tab)
sma_tree_ld_tab |>
kable() |>
kable_styling()
|
Data
|
Slope
|
Intercept
|
R2
|
|
All
|
0.96 [0.94, 0.99]
|
0.11 [0.06, 0.16]
|
0.72
|
|
Dense ~ Thick~Large
|
0.89 [0.79, 1]
|
0.25 [0.06, 0.44]
|
0.49
|
|
Dense ~ Thick~Small
|
0.91 [0.85, 0.97]
|
0.21 [0.1, 0.32]
|
0.76
|
|
Dense ~ Thin~Large
|
0.75 [0.67, 0.85]
|
0.44 [0.29, 0.6]
|
0.34
|
|
Dense ~ Thin~Small
|
0.8 [0.72, 0.9]
|
0.36 [0.2, 0.52]
|
0.65
|
|
Nondense ~ Thick~Large
|
0.74 [0.64, 0.86]
|
0.61 [0.38, 0.83]
|
0.43
|
|
Nondense ~ Thick~Small
|
0.84 [0.78, 0.91]
|
0.38 [0.24, 0.53]
|
0.68
|
|
Nondense ~ Thin~Large
|
0.73 [0.65, 0.81]
|
0.57 [0.42, 0.72]
|
0.28
|
|
Nondense ~ Thin~Small
|
0.89 [0.78, 1.01]
|
0.25 [0.03, 0.46]
|
0.38
|
Validation
tar_load(cv_sp)
cv_sp
#> $table
#> # A tibble: 3 × 3
#> model r2 mse
#> <chr> <dbl> <dbl>
#> 1 fit 1 0.866 0.0195
#> 2 fit 2 0.866 0.0196
#> 3 fit 3 0.867 0.0194
#>
#> $fit1
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(lma_disc), data = tree)
#>
#> Coefficients:
#> (Intercept) log(lma_disc)
#> 0.4852 0.9108
#>
#>
#> $fit2
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(la) + log(lt), data = tree,
#> offset = log(lma_disc))
#>
#> Coefficients:
#> (Intercept) log(la) log(lt)
#> 0.007418 0.036529 0.028880
#>
#>
#> $fit3
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(ld_leaf) + log(la) + log(lt),
#> data = tree, offset = log(lma_disc))
#>
#> Coefficients:
#> (Intercept) log(ld_leaf) log(la) log(lt)
#> 0.09834 0.06599 0.03733 0.04426
tar_load(cv_tree)
cv_tree
#> $table
#> # A tibble: 3 × 3
#> model r2 mse
#> <chr> <dbl> <dbl>
#> 1 fit 1 0.718 0.0421
#> 2 fit 2 0.684 0.0467
#> 3 fit 3 0.702 0.0440
#>
#> $fit1
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(lma_disc), data = tree)
#>
#> Coefficients:
#> (Intercept) log(lma_disc)
#> 0.8911 0.8176
#>
#>
#> $fit2
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(la) + log(lt), data = tree,
#> offset = log(lma_disc))
#>
#> Coefficients:
#> (Intercept) log(la) log(lt)
#> 0.05804 0.03071 0.05749
#>
#>
#> $fit3
#>
#> Call:
#> lm(formula = log(lma_leaf) ~ log(ld_leaf) + log(la) + log(lt),
#> data = tree, offset = log(lma_disc))
#>
#> Coefficients:
#> (Intercept) log(ld_leaf) log(la) log(lt)
#> 0.30044 0.16541 0.03573 0.11701
Leaf disc vs whole-leaf LMA (individual-level)
Divergence (species-level)
LMA and LD (species-level)
CV
Leaf support cost (species-level)
Computing Environment
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.3 (2022-03-10)
#> os Ubuntu 20.04.4 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2022-04-29
#> pandoc 2.16.2 @ /usr/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> P abind 1.4-5 2016-07-21 [?] RSPM (R 4.1.0)
#> P assertthat 0.2.1 2019-03-21 [?] RSPM (R 4.1.3)
#> backports 1.4.1 2021-12-13 [1] RSPM (R 4.1.3)
#> P base64url 1.4 2018-05-14 [?] RSPM (R 4.1.0)
#> P broom 0.7.12 2022-01-28 [?] RSPM (R 4.1.3)
#> P bslib 0.3.1 2021-10-06 [?] RSPM (R 4.1.3)
#> P cachem 1.0.6 2021-08-19 [?] RSPM (R 4.1.0)
#> P callr 3.7.0 2021-04-20 [?] CRAN (R 4.1.1)
#> P car 3.0-12 2021-11-06 [?] RSPM (R 4.1.0)
#> P carData 3.0-5 2022-01-06 [?] RSPM (R 4.1.0)
#> P cellranger 1.1.0 2016-07-27 [?] RSPM (R 4.1.3)
#> P checkmate 2.0.0 2020-02-06 [?] RSPM (R 4.1.0)
#> P cli 3.2.0 2022-02-14 [?] RSPM (R 4.1.0)
#> P clustermq 0.8.95.3 2022-01-26 [?] RSPM (R 4.1.0)
#> P cmdstanr * 0.5.1.9000 2022-04-19 [?] Github (stan-dev/cmdstanr@bfa83a4)
#> P codetools 0.2-18 2020-11-04 [?] CRAN (R 4.1.2)
#> P colorspace 2.0-3 2022-02-21 [?] RSPM (R 4.1.3)
#> crayon 1.5.1 2022-03-26 [1] RSPM (R 4.1.3)
#> P data.table 1.14.2 2021-09-27 [?] RSPM (R 4.1.3)
#> P DBI 1.1.2 2021-12-20 [?] RSPM (R 4.1.3)
#> P dbplyr 2.1.1 2021-04-06 [?] RSPM (R 4.1.3)
#> P desc 1.4.0 2021-09-28 [?] CRAN (R 4.1.1)
#> P devtools 2.4.3 2021-11-30 [?] RSPM (R 4.1.0)
#> digest 0.6.29 2021-12-01 [1] RSPM (R 4.1.3)
#> P distributional 0.3.0 2022-01-05 [?] RSPM (R 4.1.0)
#> P dplyr * 1.0.8 2022-02-08 [?] RSPM (R 4.1.3)
#> P ellipsis 0.3.2 2021-04-29 [?] CRAN (R 4.1.1)
#> evaluate 0.15 2022-02-18 [1] RSPM (R 4.1.3)
#> P extrafont * 0.17 2014-12-08 [?] RSPM (R 4.1.0)
#> P extrafontdb 1.0 2012-06-11 [?] RSPM (R 4.1.0)
#> fansi 1.0.3 2022-03-24 [1] RSPM (R 4.1.3)
#> P farver 2.1.0 2021-02-28 [?] RSPM (R 4.1.3)
#> P fastmap 1.1.0 2021-01-25 [?] CRAN (R 4.1.1)
#> P forcats * 0.5.1 2021-01-27 [?] RSPM (R 4.1.3)
#> fs 1.5.2 2021-12-08 [1] RSPM (R 4.1.3)
#> P fst 0.9.8 2022-02-08 [?] RSPM (R 4.1.0)
#> P fstcore 0.9.12 2022-03-23 [?] RSPM (R 4.1.0)
#> P generics 0.1.2 2022-01-31 [?] RSPM (R 4.1.3)
#> P ggplot2 * 3.3.5 2021-06-25 [?] RSPM (R 4.1.3)
#> P ggpubr * 0.4.0.999 2022-04-09 [?] Github (mattocci27/ggpubr@901fdeb)
#> P ggsignif 0.6.3 2021-09-09 [?] RSPM (R 4.1.0)
#> P ggsma * 0.1.0 2022-04-09 [?] Github (mattocci27/ggsma@2b56c57)
#> P glue 1.6.2 2022-02-24 [?] RSPM (R 4.1.0)
#> P gtable 0.3.0 2019-03-25 [?] RSPM (R 4.1.3)
#> P haven 2.4.3 2021-08-04 [?] RSPM (R 4.1.3)
#> P highr 0.9 2021-04-16 [?] CRAN (R 4.1.1)
#> P hms 1.1.1 2021-09-26 [?] RSPM (R 4.1.3)
#> P htmltools 0.5.2 2021-08-25 [?] CRAN (R 4.1.1)
#> P httr 1.4.2 2020-07-20 [?] CRAN (R 4.1.2)
#> P igraph 1.3.0 2022-04-01 [?] RSPM (R 4.1.0)
#> P insight 0.17.0 2022-03-29 [?] RSPM (R 4.1.0)
#> P janitor * 2.1.0 2021-01-05 [?] RSPM (R 4.1.0)
#> P jquerylib 0.1.4 2021-04-26 [?] RSPM (R 4.1.3)
#> P jsonlite 1.7.2 2020-12-09 [?] CRAN (R 4.1.1)
#> P kableExtra * 1.3.4 2021-02-20 [?] RSPM (R 4.1.0)
#> knitr * 1.38 2022-03-25 [1] RSPM (R 4.1.3)
#> P languageserver * 0.3.12 2021-10-19 [?] RSPM (R 4.1.0)
#> P lifecycle 1.0.1 2021-09-24 [?] CRAN (R 4.1.1)
#> P loo * 2.5.1 2022-03-24 [?] RSPM (R 4.1.0)
#> P lubridate 1.8.0 2021-10-07 [?] RSPM (R 4.1.3)
#> magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.1.3)
#> P matrixStats 0.61.0 2021-09-17 [?] RSPM (R 4.1.0)
#> P memoise 2.0.1 2021-11-26 [?] RSPM (R 4.1.0)
#> P modelr * 0.1.8 2020-05-19 [?] RSPM (R 4.1.3)
#> P munsell 0.5.0 2018-06-12 [?] RSPM (R 4.1.3)
#> P patchwork * 1.1.1 2020-12-17 [?] RSPM (R 4.1.0)
#> P performance * 0.9.0 2022-03-30 [?] RSPM (R 4.1.0)
#> pillar 1.7.0 2022-02-01 [1] RSPM (R 4.1.3)
#> P pkgbuild 1.3.1 2021-12-20 [?] RSPM (R 4.1.0)
#> P pkgconfig 2.0.3 2019-09-22 [?] CRAN (R 4.1.1)
#> P pkgload 1.2.2 2021-09-11 [?] CRAN (R 4.1.1)
#> P posterior 1.2.1 2022-03-07 [?] RSPM (R 4.1.0)
#> P prettyunits 1.1.1 2020-01-24 [?] RSPM (R 4.1.3)
#> processx 3.5.3 2022-03-25 [1] RSPM (R 4.1.3)
#> P ps 1.6.0 2021-02-28 [?] CRAN (R 4.1.1)
#> P purrr * 0.3.4 2020-04-17 [?] CRAN (R 4.1.1)
#> P qs 0.25.3 2022-02-22 [?] RSPM (R 4.1.0)
#> P R6 2.5.1 2021-08-19 [?] CRAN (R 4.1.1)
#> P RApiSerialize 0.1.0 2014-04-19 [?] RSPM (R 4.1.0)
#> P Rcpp 1.0.8.3 2022-03-17 [?] RSPM (R 4.1.0)
#> RcppParallel 5.1.5 2022-01-05 [1] RSPM (R 4.1.3)
#> P readr * 2.1.2 2022-01-30 [?] RSPM (R 4.1.3)
#> P readxl 1.4.0 2022-03-28 [?] RSPM (R 4.1.3)
#> P remotes 2.4.1 2021-09-29 [?] CRAN (R 4.1.1)
#> renv 0.15.4 2022-04-19 [1] Github (rstudio/renv@5ea7504)
#> P reprex 2.0.1 2021-08-05 [?] RSPM (R 4.1.3)
#> P rlang 1.0.2 2022-03-04 [?] RSPM (R 4.1.3)
#> P rmarkdown 2.13 2022-03-10 [?] RSPM (R 4.1.3)
#> P rprojroot 2.0.2 2020-11-15 [?] CRAN (R 4.1.1)
#> P rstatix 0.7.0 2021-02-13 [?] RSPM (R 4.1.0)
#> P rstudioapi 0.13 2020-11-12 [?] CRAN (R 4.1.1)
#> P Rttf2pt1 1.3.8 2020-01-10 [?] RSPM (R 4.1.0)
#> P rvest 1.0.2 2021-10-16 [?] RSPM (R 4.1.3)
#> P sass 0.4.1 2022-03-23 [?] RSPM (R 4.1.3)
#> scales 1.2.0 2022-04-13 [1] RSPM (R 4.1.3)
#> P sessioninfo 1.2.2 2021-12-06 [?] RSPM (R 4.1.0)
#> P smatr * 3.4-8 2018-03-18 [?] RSPM (R 4.1.0)
#> P snakecase 0.11.0 2019-05-25 [?] RSPM (R 4.1.0)
#> stantargets * 0.0.3.9001 2022-04-20 [1] Github (ropensci/stantargets@0df1163)
#> P stringfish 0.15.7 2022-04-13 [?] RSPM (R 4.1.0)
#> stringi 1.7.6 2021-11-29 [1] RSPM (R 4.1.3)
#> P stringr * 1.4.0 2019-02-10 [?] CRAN (R 4.1.1)
#> P svglite 2.1.0 2022-02-03 [?] RSPM (R 4.1.0)
#> P systemfonts 1.0.4 2022-02-11 [?] RSPM (R 4.1.0)
#> P tarchetypes * 0.5.0 2022-03-16 [?] RSPM (R 4.1.0)
#> P targets * 0.11.0 2022-03-19 [?] RSPM (R 4.1.0)
#> P tensorA 0.36.2 2020-11-19 [?] RSPM (R 4.1.0)
#> P testthat 3.0.4 2021-07-01 [?] CRAN (R 4.1.1)
#> tibble * 3.1.6 2021-11-07 [1] RSPM (R 4.1.3)
#> P tidyr * 1.2.0 2022-02-01 [?] RSPM (R 4.1.3)
#> P tidyselect 1.1.2 2022-02-21 [?] RSPM (R 4.1.3)
#> P tidyverse * 1.3.1 2021-04-15 [?] RSPM (R 4.1.0)
#> P tzdb 0.3.0 2022-03-28 [?] RSPM (R 4.1.3)
#> P usethis 2.1.5 2021-12-09 [?] RSPM (R 4.1.0)
#> P utf8 1.2.2 2021-07-24 [?] CRAN (R 4.1.1)
#> vctrs 0.4.1 2022-04-13 [1] RSPM (R 4.1.3)
#> P viridisLite 0.4.0 2021-04-13 [?] RSPM (R 4.1.3)
#> P webshot 0.5.2 2019-11-22 [?] RSPM (R 4.1.0)
#> P withr 2.5.0 2022-03-03 [?] RSPM (R 4.1.0)
#> P xfun 0.30 2022-03-02 [?] RSPM (R 4.1.3)
#> P xml2 1.3.3 2021-11-30 [?] CRAN (R 4.1.2)
#> yaml 2.3.5 2022-02-21 [1] RSPM (R 4.1.3)
#>
#> [1] /home/mattocci/leaf-disc/renv/library/linux-ubuntu-focal/R-4.1/x86_64-pc-linux-gnu
#> [2] /usr/local/lib/R/library
#>
#> P ── Loaded and on-disk path mismatch.
#>
#> ──────────────────────────────────────────────────────────────────────────────
tar_visnetwork()
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
#> ✔ ggplot2 3.3.5 ✔ purrr 0.3.4
#> ✔ tibble 3.1.6 ✔ dplyr 1.0.8
#> ✔ tidyr 1.2.0 ✔ stringr 1.4.0
#> ✔ readr 2.1.2 ✔ forcats 0.5.1
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag() masks stats::lag()
#> This is cmdstanr version 0.5.1.9000
#> - CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
#> - CmdStan path: /opt/cmdstan/cmdstan-2.29.0
#> - CmdStan version: 2.29.0
#>
#> A newer version of CmdStan is available. See ?install_cmdstan() to install it.
#> To disable this check set option or environment variable CMDSTANR_NO_VER_CHECK=TRUE.
#> CmdStan path set to: /opt/cmdstan/cmdstan-2.29.0